Genetic Diversity and Transmission Characteristics of Beijing Family Strains of Mycobacterium tuberculosis in Peru Tomotada Iwamoto 1 *, Louis Grandjean 2,3,4 , Kentaro Arikawa 1 , Noriko Nakanishi 1 , Luz Caviedes 4 , Jorge Coronel 4 , Patricia Sheen 4 , Takayuki Wada 5 , Carmen A. Taype 6 , Marie-Anne Shaw 6 , David A. J. Moore 3,4 , Robert H. Gilman 4,7 1 Department of Microbiology, Kobe Institute of Health, Kobe, Japan, 2 Wellcome Centre for Clinical Tropical Medicine, St. Mary’s Campus, Imperial College, London, United Kingdom, 3 Clinical Research Department and TB Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom, 4 Laboratorio de Investigacio ´ n de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru, 5 Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, Osaka, Japan, 6 Faculty of Biological Science, University of Leeds, Leeds, United Kingdom, 7 Department of International Health, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, United States of America Abstract Beijing family strains of Mycobacterium tuberculosis have attracted worldwide attention because of their wide geographical distribution and global emergence. Peru, which has a historical relationship with East Asia, is considered to be a hotspot for Beijing family strains in South America. We aimed to unveil the genetic diversity and transmission characteristics of the Beijing strains in Peru. A total of 200 Beijing family strains were identified from 2140 M. tuberculosis isolates obtained in Lima, Peru, between December 2008 and January 2010. Of them, 198 strains were classified into sublineages, on the basis of 10 sets of single nucleotide polymorphisms (SNPs). They were also subjected to variable number tandem-repeat (VNTR) typing using an international standard set of 15 loci (15-MIRU-VNTR) plus 9 additional loci optimized for Beijing strains. An additional 70 Beijing family strains, isolated between 1999 and 2006 in Lima, were also analyzed in order to make a longitudinal comparison. The Beijing family was the third largest spoligotyping clade in Peru. Its population structure, by SNP typing, was characterized by a high frequency of Sequence Type 10 (ST10), which belongs to a modern subfamily of Beijing strains (178/198, 89.9%). Twelve strains belonged to the ancient subfamily (ST3 [n = 3], ST25 [n = 1], ST19 [n = 8]). Overall, the polymorphic information content for each of the 24 loci values was low. The 24 loci VNTR showed a high clustering rate (80.3%) and a high recent transmission index (RTI n21 = 0.707). These strongly suggest the active and on- going transmission of Beijing family strains in the survey area. Notably, 1 VNTR genotype was found to account for 43.9% of the strains. Comparisons with data from East Asia suggested the genotype emerged as a uniquely endemic clone in Peru. A longitudinal comparison revealed the genotype was present in Lima by 1999. Citation: Iwamoto T, Grandjean L, Arikawa K, Nakanishi N, Caviedes L, et al. (2012) Genetic Diversity and Transmission Characteristics of Beijing Family Strains of Mycobacterium tuberculosis in Peru. PLoS ONE 7(11): e49651. doi:10.1371/journal.pone.0049651 Editor: Igor Mokrousov, St. Petersburg Pasteur Institute, Russian Federation Received August 5, 2012; Accepted October 11, 2012; Published November 21, 2012 Copyright: ß 2012 Iwamoto et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by Health Science Research grants(H24-SHINKO-IPPAN-011) from Ministry of Health, Labour and Welfare of Japan, MEXT/JSPS KAKENHI Grant Number 24590845, R24 TW007988 NIH FIC, D43 TW006581 NIH FIC, RO1 HD059005 NIH NICHD, WT088559MA with the Wellcome Trust, Wellcome Trust grant 078067/Z/05, a research grant of the Institute for Fermentation, Osaka, Japan, and the US-Japan Cooperative Medical Science Program (TB and Leprosy panel). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: kx2t-iwmt@asahi-net.or.jp Introduction Strains of the Beijing family of Mycobacterium tuberculosis (M. tuberculosis), first described in 1995 [1], have attracted worldwide attention because of their wide geographical distribution and global emergence. These strains have also been shown to have an endemic prevalence in certain regions, including Asia, except for the Indian subcontinent; northern Eurasia; and South Africa [2,3,4,5,6,7]. The lineage has been reported to have caused major outbreaks worldwide, some involving drug-resistant variants [2,8,9]. These characteristics suggest that strains belonging to this family might have selective advantages (higher virulence or transmissibility) over other M. tuberculosis strains [10,11,12,13]. Therefore, a better understanding of the contribution of the Beijing family to the tuberculosis (TB) pandemic is vital to improve global TB control. The Beijing family is reported to be phylogenetically divisible into 2 main subfamilies: the modern (typical) and ancient (atypical) subfamilies, [14,15]. The modern subfamily is highly prevalent in China, western Russia, South Africa, and Thailand [3,15,16,17], whereas the ancient subfamily, with a deleted region of difference (RD) RD181[-] (late ancient type), is endemic in Japan and the ancient subfamily with RD181[+] (early ancient type) is endemic in Korea [4,18,19,20,21,22,23,24]. Although the reasons for the phylogeographical differences remain elusive, the above trends can be used to assess the influence of the Beijing family strains from East Asian countries, where the prevalence is very high [2,3], on the prevalence of Beijing family strains in other regions. In fact, a PLOS ONE | www.plosone.org 1 November 2012 | Volume 7 | Issue 11 | e49651